Problem with "Separate by Watershed" roi tool

Hi,
It looks like there is a bug with the new separate by Watershed ROI tool. I segmented nuclei with HK mean plugin, then select ROI with two nuclei and click separate by watershed and the selected ROI disappears. If I dilate the ROI before and then use watershed, it works…
Best.

Stéphane

Dear Stéphane,

Could you upload a test image and indicate the parameters you used for HK-Means, so that we can reproduce and test this issue?

Many thanks in advance!
Best regards,
Marion

Here are the HK-means parameters:
image

BON-VMAT2-PMA-Glc.lif - BON-VMAT2-rest-aGFP-d1000003.tif (5.3 MB)

Dear Stéphane,

Thank you for the test image and HK-Means parameters.

Indeed I can reproduce this bug. I invite @dgonzale to join this discusion.

To give details to Daniel and everyone else, after the HK-Means segmentation, I obtain this:

When I click on Separate by Watershed, the selected ROI is deleted:

If, after the HK-Means, I first dilate (by 1.0 pixel) and then Separate by Watershed, I obtain these 4 ROIs:

Best regards,
Marion

Hello @Stephane_Ory ,
Looking at @MarionLouveaux example, this behavior is expected because there are holes in your segmentation, try using the fill holes plugin before using the watershed separation.
Best,

Daniel Gonzalez

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Hi @MarionLouveaux and @dgonzale,

Thank you for your answers.
I already tried to fill holes before watershed, but it doesn’t change the issue. The selected ROI disappears.
Best.

Stéphane

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Hello @Stephane_Ory ,
You are right, the ROI disappears. Thank you for noticing it, I just found a bug when computing the distance map of the ROI. I will fix it ASAP. In the mean time, you can try setting the channel associated to the target ROI to 0 or All on the ROI explorer panel (the tab called ROIs on the right of the UI).

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